PhD Chapter 1
Global - Maps and exploration
This series of files compile analyses done for the global analysis of Chapter 1 (version of May 15th).
All analyses have been done with PRIMER-e 6 and R 4.1.2.
Click on the table of contents in the left margin to assess a specific analysis.
Click on a figure to zoom it
We used data from subtidal ecosystems (see metadata files for more information). Only stations that have been sampled both for abiotic parameters and benthic species were included.
Selected variables for the analyses:
- Bathymetry: depth
- Percentage of organic matter: om
- Percentage of gravel: gravel
- Percentage of sand: sand
- Percentage of silt: silt
- Percentage of clay: clay
- Concentration of arsenic: arsenic
- Concentration of cadmium: cadmium
- Concentration of chromium: chromium
- Concentration of copper: copper
- Concentration of iron: iron
- Concentration of manganese: manganese
- Concentration of mercury: mercury
- Concentration of lead: lead
- Concentration of zinc: zinc
- Specific richness: S
- Total density of individuals: N
- Shannon’s diversity: H
- Piélou’s evenness: J
1. Statistics
Calculation of basic statistics for each variable considered (apart from species densities):
| Mean | SD | SE | Median | Min | Max | 95% CI | |
|---|---|---|---|---|---|---|---|
| depth | 22.362 | 18.426 | 1.184 | 18.250 | 1.000 | 77.000 | 2.321 |
| om | 1.168 | 1.072 | 0.069 | 0.810 | 0.168 | 8.260 | 0.135 |
| gravel | 0.035 | 0.115 | 0.007 | 0.000 | 0.000 | 0.809 | 0.014 |
| sand | 0.527 | 0.360 | 0.023 | 0.562 | 0.000 | 1.001 | 0.045 |
| silt | 0.273 | 0.285 | 0.018 | 0.152 | 0.000 | 0.942 | 0.036 |
| clay | 0.165 | 0.348 | 0.022 | 0.000 | 0.000 | 1.000 | 0.044 |
| Mean | SD | SE | Median | Min | Max | 95% CI | |
|---|---|---|---|---|---|---|---|
| arsenic | 3.559 | 2.568 | 0.194 | 2.700 | 0.80 | 21.30 | 0.380 |
| cadmium | 0.133 | 0.039 | 0.003 | 0.130 | 0.03 | 0.27 | 0.006 |
| chromium | 57.992 | 21.914 | 1.657 | 54.000 | 10.90 | 143.30 | 3.247 |
| copper | 11.205 | 6.436 | 0.486 | 9.900 | 2.20 | 32.40 | 0.953 |
| iron | 55387.011 | 21175.992 | 1600.755 | 53398.800 | 14089.92 | 188857.22 | 3137.421 |
| manganese | 1148.868 | 711.475 | 53.782 | 959.400 | 251.67 | 5962.19 | 105.412 |
| mercury | 0.021 | 0.025 | 0.002 | 0.017 | 0.00 | 0.25 | 0.004 |
| lead | 5.030 | 2.400 | 0.181 | 4.900 | 1.02 | 12.20 | 0.356 |
| zinc | 57.614 | 21.047 | 1.591 | 52.900 | 15.90 | 141.40 | 3.118 |
| Mean | SD | SE | Median | Min | Max | 95% CI | |
|---|---|---|---|---|---|---|---|
| S | 14.277 | 6.877 | 0.534 | 13.000 | 1 | 35.000 | 1.046 |
| N | 225.910 | 424.411 | 32.941 | 74.000 | 1 | 2103.000 | 64.563 |
| H | 1.787 | 0.509 | 0.039 | 1.861 | 0 | 2.737 | 0.077 |
| J | 0.710 | 0.173 | 0.013 | 0.727 | 0 | 1.000 | 0.026 |
| delta | 51.995 | 13.129 | 1.019 | 54.733 | 0 | 77.778 | 1.997 |
| delta_plus | 69.141 | 6.425 | 0.499 | 70.152 | 0 | 77.778 | 0.977 |
| delta_star | 68.918 | 9.047 | 0.702 | 71.373 | 0 | 79.812 | 1.376 |
| Mean | SD | SE | Median | Min | Max | 95% CI | |
|---|---|---|---|---|---|---|---|
| S | 7.579 | 4.435 | 0.312 | 7.000 | 0 | 19.000 | 0.612 |
| N | 39.624 | 61.123 | 4.301 | 24.500 | 0 | 674.000 | 8.429 |
| H | 1.417 | 0.640 | 0.045 | 1.482 | 0 | 2.646 | 0.088 |
| J | 0.750 | 0.232 | 0.016 | 0.823 | 0 | 1.000 | 0.032 |
| delta | 55.227 | 19.863 | 1.398 | 59.778 | 0 | 87.500 | 2.739 |
| delta_plus | 76.490 | 17.269 | 1.215 | 80.253 | 0 | 87.500 | 2.381 |
| delta_star | 76.147 | 17.664 | 1.243 | 80.398 | 0 | 88.001 | 2.436 |
2. Maps
2.1. General maps
All stations were not necessarily sampled for every variable characterization:
Habitat
Metals
0.5 mm community
1 mm community
2.2. Parameters maps
For maps of heavy metal concentrations, stations have been grouped based on Environment Canada (2007) classification of sediment toxicity (grey = low toxicity, red = high toxicity).
Depth
OM
Gravel
Sand
Silt
Clay
Arsenic
Cadmium
Chromium
Copper
Iron
Manganese
Mercury
Lead
Zinc
Richness (0.5 mm)
Density (0.5 mm)
Diversity (0.5 mm)
Evenness (0.5 mm)
Distinctness (0.5 mm)
Richness (1 mm)
Density (1 mm)
Diversity (1 mm)
Evenness (1 mm)
Distinctness (1 mm)
3. Figures
3.1. Phylum frequencies
| phylum | sp500 | sp1000 |
|---|---|---|
| Annelida | 24802 | 2125 |
| Arthropoda | 6532 | 3066 |
| Mollusca | 2899 | 1765 |
| Nematoda | 1377 | 165 |
| Phoronida | 1140 | 0 |
| Echinodermata | 579 | 828 |
| Cnidaria | 86 | 6 |
| Sipuncula | 32 | 27 |
| Bryozoa | 30 | 0 |
| Nemertea | 21 | 17 |
| Hemichordata | 2 | 0 |
| Chaetognatha | 1 | 0 |
| Brachiopoda | 0 | 2 |
| Platyhelminthes | 0 | 3 |
3.2. Species estimation curves
0.5 mm community
1 mm community
3.3. Hierarchical Agglomerative Clustering
We used the Ward method for the clustering. To determine the number of clusters, we used multiple methods such as K-means, Elbow or Silhouette.
0.5 mm community
Species densities have been transformed with a (log+1) operation. Three clusters have been determined.
1 mm community
Species densities have been transformed with a (log+1) operation. Stations with 0 or 1 individuals (80, 88 and 130) have been deleted, as they were serious outliers for the plot. Three clusters have been determined.
Habitat
Variables have been standardized by mean and standard-deviation. Three clusters have been determined.
| KL | CH | Hartigan | CCC | Scott | Marriot | TrCovW | TraceW | Friedman | Rubin | Cindex | DB | Silhouette | Duda | Pseudot2 | Beale | Ratkowsky | Ball | Ptbiserial | Frey | McClain | Dunn | Hubert | SDindex | Dindex | SDbw | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 2 | 0.348 | 87.96 | 123 | -0.3129 | 414.1 | 163701142 | 53731 | 1058 | 348171 | 1.367 | 0.3017 | 1.62 | 0.3108 | 0.4783 | 141.8 | 4.165 | 0.3341 | 529.1 | 0.364 | -0.2151 | 0.6873 | 0.0397 | 0.001 | 4.156 | 1.824 | 1.249 |
| 3 | 4.659 | 127.5 | 43.53 | 5.9 | 1176 | 15810870 | 23337 | 699.7 | 727290 | 2.067 | 0.2559 | 1.151 | 0.4163 | 0.7095 | 44.22 | 1.561 | 0.3882 | 233.2 | 0.552 | 0.8877 | 0.8536 | 0.0422 | 0.0015 | 3.401 | 1.421 | 0.9941 |
| 4 | 0.9699 | 114.5 | 39.56 | 6.339 | 1315 | 15835079 | 16978 | 591.9 | 747758 | 2.443 | 0.2341 | 1.319 | 0.3753 | 0.6644 | 47.98 | 1.923 | 0.3736 | 148 | 0.5172 | 0.319 | 1.287 | 0.0367 | 0.0015 | 3.469 | 1.263 | 0.7754 |
| 5 | 0.3773 | 109.6 | 85.46 | 8.768 | 1529 | 10227492 | 13762 | 507.6 | 754553 | 2.849 | 0.2067 | 1.233 | 0.3677 | 0.4478 | 59.19 | 4.647 | 0.3516 | 101.5 | 0.5196 | -0.1354 | 1.563 | 0.0367 | 0.0016 | 3.017 | 1.143 | 0.6224 |
| 6 | 2.123 | 135.8 | 50.24 | 18.94 | 1849 | 3922592 | 7501 | 373 | 792347 | 3.876 | 0.1929 | 1.008 | 0.3921 | 0.5648 | 56.26 | 2.925 | 0.3477 | 62.17 | 0.5594 | 0.3042 | 1.479 | 0.0379 | 0.002 | 2.865 | 1.038 | 0.4619 |
| 7 | 1.609 | 145 | 36.34 | 23.2 | 2015 | 2687470 | 4654 | 307.6 | 812181 | 4.701 | 0.1624 | 1.01 | 0.416 | 0.4665 | 37.74 | 4.27 | 0.3339 | 43.94 | 0.5495 | 0.2203 | 1.711 | 0.0379 | 0.0021 | 2.681 | 0.9332 | 0.4498 |
| 8 | 1.425 | 148 | 28.61 | 25.6 | 2127 | 2209821 | 3377 | 266.4 | 812290 | 5.429 | 0.1959 | 1.007 | 0.4131 | 0.4943 | 44 | 3.847 | 0.3188 | 33.3 | 0.5485 | 0.2616 | 1.75 | 0.0484 | 0.0022 | 2.49 | 0.8648 | 0.3749 |
| 9 | 0.6684 | 148.3 | 40.7 | 27.1 | 2383 | 969494 | 2879 | 237.3 | 849061 | 6.092 | 0.1808 | 0.9757 | 0.4274 | 0.6047 | 27.46 | 2.457 | 0.3041 | 26.37 | 0.5431 | 0.1772 | 1.815 | 0.0484 | 0.0022 | 2.402 | 0.8068 | 0.3446 |
| 10 | 2.595 | 158.7 | 20.55 | 30.56 | 2567 | 560685 | 2031 | 202.1 | 860092 | 7.157 | 0.1573 | 0.9431 | 0.4387 | 0.404 | 41.31 | 5.48 | 0.2928 | 20.21 | 0.5412 | 0.3612 | 1.831 | 0.0484 | 0.0023 | 2.253 | 0.749 | 0.3775 |
| 11 | 0.477 | 156.9 | 37.48 | 31.24 | 2630 | 522523 | 1623 | 185.6 | 862272 | 7.79 | 0.15 | 0.9328 | 0.4268 | 1.696 | -4.925 | -1.458 | 0.2812 | 16.87 | 0.5331 | -0.0598 | 1.88 | 0.0484 | 0.0024 | 2.367 | 0.7074 | 0.3243 |
| 12 | 8.916 | 168.4 | 9.688 | 34.49 | 2775 | 341016 | 1219 | 159.7 | 862633 | 9.055 | 0.1717 | 0.827 | 0.4362 | 0.6722 | 28.29 | 1.845 | 0.2721 | 13.31 | 0.5359 | 1.725 | 1.853 | 0.0564 | 0.0024 | 2.366 | 0.6796 | 0.2497 |
| 13 | 0.1458 | 161 | 32.03 | 33.86 | 2816 | 337862 | 1112 | 153.2 | 867543 | 9.436 | 0.1641 | 0.9034 | 0.3891 | 0.5433 | 15.97 | 3.072 | 0.2621 | 11.79 | 0.479 | 0.0346 | 2.341 | 0.0564 | 0.0025 | 4.094 | 0.656 | 0.1942 |
| 14 | 3.264 | 171.1 | 13.6 | 36.57 | 2965 | 212308 | 827 | 134.4 | 874808 | 10.76 | 0.1989 | 0.9339 | 0.3974 | 0.5919 | 20.68 | 2.567 | 0.2544 | 9.603 | 0.4823 | 0.4409 | 2.272 | 0.0724 | 0.0025 | 4.066 | 0.6358 | 0.193 |
| 15 | 1.019 | 168.6 | 13.32 | 36.76 | 3018 | 195826 | 718.8 | 126.9 | 876361 | 11.4 | 0.1874 | 0.9609 | 0.396 | 0.451 | 25.57 | 4.471 | 0.2465 | 8.458 | 0.4665 | 0.341 | 2.396 | 0.0724 | 0.0025 | 4.161 | 0.6108 | 0.1718 |
Metals
Variables have been standardized by mean and standard-deviation. Two clusters have been determined.
| KL | CH | Hartigan | CCC | Scott | Marriot | TrCovW | TraceW | Friedman | Rubin | Cindex | DB | Silhouette | Duda | Pseudot2 | Beale | Ratkowsky | Ball | Ptbiserial | Frey | McClain | Dunn | Hubert | SDindex | Dindex | SDbw | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 2 | 4.327 | 114 | 36.77 | -2.685 | 213.4 | 1.65e+16 | 10239 | 944 | 39.94 | 1.659 | 0.2354 | 1.232 | 0.3851 | 0.6987 | 32.34 | 2.556 | 0.4311 | 472 | 0.4259 | 0.1581 | 0.5802 | 0.0617 | 8e-04 | 2.029 | 1.869 | 1.441 |
| 3 | 1.13 | 86.98 | 30.74 | -3.299 | 403.7 | 1.251e+16 | 9284 | 778.5 | 49.88 | 2.011 | 0.2243 | 1.441 | 0.3188 | 0.701 | 40.94 | 2.535 | 0.3974 | 259.5 | 0.4783 | 0.2355 | 0.7284 | 0.0663 | 0.0012 | 2.434 | 1.703 | 1.204 |
| 4 | 3.334 | 78.14 | 14.58 | -2.483 | 595.3 | 7.444e+15 | 5946 | 660.5 | 55.93 | 2.371 | 0.1892 | 1.434 | 0.3406 | 0.6838 | 37 | 2.743 | 0.3748 | 165.1 | 0.5184 | 3.424 | 0.9056 | 0.0663 | 0.0013 | 2.366 | 1.583 | 1.038 |
| 5 | 1.054 | 66.86 | 12.71 | -3.035 | 667 | 7.721e+15 | 5413 | 608.6 | 60.54 | 2.573 | 0.1818 | 1.414 | 0.2377 | 0.7734 | 14.94 | 1.725 | 0.3456 | 121.7 | 0.4324 | 0.7738 | 1.468 | 0.0418 | 0.0014 | 2.72 | 1.489 | 1.077 |
| 6 | 0.3482 | 59.67 | 23.64 | -3.385 | 741.5 | 7.263e+15 | 5003 | 566.3 | 63.44 | 2.765 | 0.1817 | 1.56 | 0.1993 | 0.6471 | 12 | 3.133 | 0.324 | 94.38 | 0.4056 | -0.0512 | 1.844 | 0.0446 | 0.0015 | 2.703 | 1.412 | 0.836 |
| 7 | 3.966 | 60.26 | 9.604 | -1.462 | 935.8 | 3.258e+15 | 3941 | 496.8 | 71 | 3.152 | 0.1686 | 1.498 | 0.2216 | 0.6456 | 30.19 | 3.237 | 0.3102 | 70.97 | 0.4231 | 1.721 | 1.804 | 0.0446 | 0.0016 | 2.764 | 1.343 | 0.8493 |
| 8 | 0.2883 | 55.64 | 21.61 | -1.329 | 1005 | 2.868e+15 | 3674 | 469.9 | 74.03 | 3.332 | 0.162 | 1.509 | 0.2139 | 0.5388 | 20.55 | 4.935 | 0.294 | 58.74 | 0.3715 | -0.0064 | 2.473 | 0.0446 | 0.0017 | 3.131 | 1.28 | 0.6832 |
| 9 | 1.098 | 57.34 | 21 | 1.181 | 1133 | 1.744e+15 | 2600 | 416.1 | 76.29 | 3.764 | 0.1897 | 1.328 | 0.2213 | 0.5854 | 9.917 | 3.97 | 0.285 | 46.23 | 0.3833 | -0.0608 | 2.418 | 0.0566 | 0.0017 | 3.161 | 1.231 | 0.7533 |
| 10 | 1.15 | 59.39 | 19.66 | 3.634 | 1375 | 5.395e+14 | 2077 | 369.4 | 85.89 | 4.24 | 0.1825 | 1.255 | 0.2353 | 0.2913 | 14.6 | 12.52 | 0.2761 | 36.94 | 0.3903 | -0.037 | 2.362 | 0.0566 | 0.0018 | 3.054 | 1.178 | 0.6423 |
| 11 | 0.8698 | 61.41 | 23.87 | 5.892 | 1564 | 2.216e+14 | 1611 | 330 | 95.33 | 4.745 | 0.1791 | 1.17 | 0.2487 | 1.495 | -0.9929 | -1.49 | 0.2674 | 30 | 0.3932 | -0.0856 | 2.339 | 0.0566 | 0.0018 | 2.776 | 1.121 | 0.532 |
| 12 | 1.306 | 65.72 | 20.27 | 8.912 | 1737 | 9.806e+13 | 1322 | 288.1 | 101.4 | 5.435 | 0.1872 | 1.059 | 0.2654 | 0.5018 | 11.91 | 5.502 | 0.2605 | 24.01 | 0.3949 | 0.023 | 2.325 | 0.0597 | 0.0019 | 2.465 | 1.069 | 0.3011 |
| 13 | 1.94 | 69 | 12.07 | 11.34 | 1863 | 5.623e+13 | 942.1 | 256.3 | 107.5 | 6.111 | 0.1804 | 1.03 | 0.2768 | 0.2741 | 39.72 | 14.91 | 0.2535 | 19.71 | 0.3987 | 0.1664 | 2.3 | 0.0597 | 0.0019 | 2.447 | 1.032 | 0.287 |
| 14 | 0.3842 | 68.94 | 30.93 | 12.35 | 1961 | 3.722e+13 | 782.8 | 238.5 | 112 | 6.566 | 0.1759 | 0.9842 | 0.2656 | 0.8986 | 1.58 | 0.6324 | 0.246 | 17.03 | 0.3982 | -0.0703 | 2.317 | 0.0597 | 0.0019 | 2.561 | 0.9877 | 0.2443 |
| 15 | 2.956 | 78.03 | 12.46 | 16.6 | 2129 | 1.632e+13 | 546.8 | 200.1 | 122.7 | 7.828 | 0.3138 | 0.904 | 0.2788 | 0.6027 | 15.16 | 3.794 | 0.2411 | 13.34 | 0.4036 | 0.3758 | 2.263 | 0.1098 | 0.002 | 2.3 | 0.9477 | 0.2017 |
3.4. Principal Component Analysis
Habitat
Variables have been standardized by mean and standard-deviation.
Metals
Variables have been standardized by mean and standard-deviation.
3.5. Non-metric Multidimensional Scaling
0.5 mm community
Species densities have been transformed with a (log+1) operation.
1 mm community
Species densities have been transformed with a (log+1) operation. Stations with 0 or 1 individuals (80, 88 and 130) have been deleted, as they were serious outliers for the plot.
Habitat
Variables have been standardized by mean and standard-deviation.
Metals
Variables have been standardized by mean and standard-deviation.